R Notebook

source("labels_screws_functions.R", local = TRUE)

left_rod_df %>%
  as_tibble() %>%
  arrange(V2) %>%
  as.matrix()

             V1        V2
 [1,] 0.5264916 0.5034615 0.1956699
 [3,] 0.4511795 0.2193301
 [4,] 0.4509162 0.2485389
 [5,] 0.4511721 0.2783970
 [6,] 0.4500000 0.3150000
 [7,] 0.4550000 0.3550000
 [8,] 0.4546403
 [9,] 0.4544356 0.4214511
[10,] 0.4544356 0.4564511
[11,] 0.4932379
[12,] 0.4600000 0.5300000
[13,] 0.4600000 0.5650000
[14,] 0.4600000 0.5950000
[15,] 0.6267241
[16,] 0.4611721 0.6583970
[17,] 0.4611721 0.6883970
[18,] 0.7133970
[19,] 0.4611721 0.7383970
[20,] 0.4611721 0.7633970
[21,] 0.4778349 0.7870897
[22,] 0.4581721 0.4778349 0.8040897
[24,] 0.8210897
[25,] 0.4778349
[26,] 0.4692306 0.8564581
[27,] 0.4645770 0.8643989
[28,] 0.4699970 0.8809878
[29,] 0.4725000 0.9070000

ILIAC

left_rod_df

           [,1]      [,2]
 [1,] 0.4725000 0.9070000
 [2,] 0.4699970 0.8809878
 [3,] 0.4645770 0.8643989
 [4,] 0.4692306 0.8564581
 [5,] 0.4778349
 [6,] 0.4778349 0.8210897
 [7,] 0.4778349 0.8040897 0.4778349 0.7870897 0.4581721 0.4611721 0.7633970
[11,] 0.4611721 0.7383970 0.4611721 0.7133970
[13,] 0.4611721 0.6883970
[14,] 0.6583970
[15,] 0.4605119 0.6267241
[16,] 0.4600000 0.5650000
[18,] 0.5300000
[19,] 0.4546403 0.4564511
[21,] 0.4544356 0.4214511 0.4546403 0.3832379
[23,] 0.4550000 0.3550000
[24,] 0.4500000 0.3150000
[25,] 0.4511721
[26,] 0.4509162 0.2485389
[27,] 0.4511795
[28,] 0.4444615
[29,] 0.4664916 0.1608256

RODS

ggdraw() +
      draw_image(spine_png, scale = 1, y = 0, valign = 0, x = 0, width = 1) +
      draw_text(text = labels_df$labels, x = labels_df$x_left, y = labels_df$y, size = 12, fontface = "bold") +
      draw_text(text = labels_df$labels, x = labels_df$x_right, y = labels_df$y, size = 12, fontface = "bold") +
      geom_point(aes(x = 0.5 - iliac_x_offset, y = iliac_y), size = 4) + 
  geom_point(aes(x = 0.5 - s2ai_x_offset, y = s2ai_y), size = 4) + 
  geom_sf(data = l2_upgoing_hooks_collection) +
  ggpattern::geom_sf_pattern(data = s2ai_screw_screwhead$left_screw_sf, pattern = "stripe",  pattern_fill = "red",alpha = 0.8, pattern_colour = "blue", pattern_density = 0.01, pattern_spacing = 0.003, angle = 70) +
  ggpattern::geom_sf_pattern(data = s2ai_screw_screwhead$right_screw_sf, pattern = "stripe",  pattern_fill = "red",alpha = 0.8, pattern_colour = "blue", pattern_density = 0.01, pattern_spacing = 0.003, angle = 70) +
  theme_minimal_grid()  +
  ylim(0, 0.5)

Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Ignoring unknown parameters: angleIgnoring unknown parameters: angleScale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale.

ggdraw() +
      draw_image(spine_png, scale = 1, y = 0, valign = 0, x = 0, width = 1) +
      draw_text(text = labels_df$labels, x = labels_df$x_left, y = labels_df$y, size = 12, fontface = "bold") +
      draw_text(text = labels_df$labels, x = labels_df$x_right, y = labels_df$y, size = 12, fontface = "bold") +
      geom_point(aes(x = 0.5 - iliac_x_offset, y = iliac_y), size = 4) + 
  geom_point(aes(x = 0.5 - s2ai_x_offset, y = s2ai_y), size = 4) + 
  geom_sf(data = pedicle_hooks_collection) +
  ggpattern::geom_sf_pattern(data = s2ai_screw_screwhead$left_screw_sf, pattern = "stripe",  pattern_fill = "red",alpha = 0.8, pattern_colour = "blue", pattern_density = 0.01, pattern_spacing = 0.003, angle = 70) +
  ggpattern::geom_sf_pattern(data = s2ai_screw_screwhead$right_screw_sf, pattern = "stripe",  pattern_fill = "red",alpha = 0.8, pattern_colour = "blue", pattern_density = 0.01, pattern_spacing = 0.003, angle = 70) +
  theme_minimal_grid() 

Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Ignoring unknown parameters: angle

GET PEDICLE Y values

xy_lines <- tibble(x_left = 0.45, x_right = 0.55, y = seq(from = 0, to = 1, by = 0.01))

xy_lines

ggdraw() +
      draw_image(spine_png, scale = 1, y = 0, valign = 0, x = 0, width = 1) +
      draw_text(text = labels_df$labels, x = labels_df$x_left, y = labels_df$y, size = 12, fontface = "bold") +
      draw_text(text = labels_df$labels, x = labels_df$x_right, y = labels_df$y, size = 12, fontface = "bold") +
      geom_point(aes(x = 0.5 - iliac_x_offset, y = iliac_y), size = 4) + 
  geom_linerange(data = xy_lines, aes(xmin = x_left, xmax = x_right, y = y, color = y)) +
  draw_text(text = xy_lines$y, x = xy_lines$x_left - 0.05, y = xy_lines$y, size = 7) +
  # geom_text(data = xy_lines,  aes())
  geom_sf(data = pedicle_hooks_collection) +
  ggpattern::geom_sf_pattern(data = s2ai_screw_screwhead$left_screw_sf, pattern = "stripe",  pattern_fill = "red",alpha = 0.8, pattern_colour = "blue", pattern_density = 0.01, pattern_spacing = 0.003, angle = 70) +
  ggpattern::geom_sf_pattern(data = s2ai_screw_screwhead$right_screw_sf, pattern = "stripe",  pattern_fill = "red",alpha = 0.8, pattern_colour = "blue", pattern_density = 0.01, pattern_spacing = 0.003, angle = 70) +
  theme_minimal_grid() +
  ylim(0, 0.5)
  
  

read in coordinates csv’s

tp_hooks_df <- tp_hooks_list_df %>%
  left_join(tp_hook_heads_list_df)

Joining, by = c("level", "side", "implant_type")

l3_pedicle_y

Error: object 'l3_pedicle_y' not found

implant_starts_df %>%
  tabyl(implant)

            implant  n    percent
 lateral_mass_screw 12
         pars_screw  2 0.01315789
      pedicle_screw 48       pelvic_screw 0.05263158
            tp_hook 34 0.22368421
 translaminar_screw 48 0.31578947

tabyl(implant_starts_df$implant)

 implant_starts_df$implant  n
    laminar_downgoing_hook   0.192
      laminar_upgoing_hook 48   0.192
        lateral_mass_screw 12   0.048
            occiptal_screw  2   0.008
                pars_screw  2   0.008
             pedicle_screw 48   0.192              pelvic_screw  8   0.032
                   tp_hook 34   0.136
        translaminar_screw 48

right_vector

[1] "L1_right_pedicle_screw" "no_screw"               "L5_right_pedicle_screw"

 ggdraw() +
  draw_image(image = spine_png, x = 0, y = 0, width = 1, valign = 0, clip = "off") + 
                   ggpattern::geom_sf_pattern(
                    data = decompression_levels_sf,
                    pattern = "stripe",
                    pattern_fill = "grey",
                    alpha = 0.8,
                    pattern_colour = "red",
                    pattern_density = 0.02,
                    pattern_spacing = 0.1
                   )

Coordinate system already present. Adding new coordinate system, which will replace the existing one.

#pedicle hooks
implant_starts_df %>%
  filter(implant == "pedicle_screw")

build_pedicle_hook_function <- function(x_start, y_start){
  
  y_lenth <- 0.01
  
  x_width <- 0.012
  
  if(x_start < 0.5){
    start <- c(x_start, y_start)
    
    point_2 <- c(start[1], start[2] - y_lenth)
    
    point_3 <- c(start[1] + x_width*0.5, start[2] - y_lenth)
    
    point_5 <- point_3
    
    point_6 <- c(point_2[1] + x_width, point_2[2])
    
    
    
    hook_sf <- st_buffer(hook, dist = 0.002, endCapStyle = "ROUND")
  
    if(x_start > 0.5){
    start <- c(x_start, y_start)
    
    point_2 <- c(start[1], start[2] - y_lenth)
    
    point_3 <- c(start[1] - x_width*0.5, start[2] - y_lenth)
    
    
    point_5 <- point_3
    
    point_6 <- c(point_2[1] - x_width, point_2[2])
    point_7 <- c(point_6[1], point_6[2] + y_lenth*0.75)
    
    hook <- st_linestring(rbind(start, point_3, point_4, point_5, point_6, point_7))
    
  
  return(hook_sf)

}

implant_starts_df %>%
  filter(implant == "pedicle_hook")

pedicle_hook_df <- implant_starts_df %>%
  filter(implant == "pedicle_hook") %>%
  mutate(hook = pmap(list(..1 = x,
                          ..2 = y), .f = ~build_pedicle_hook_function(x_start = ..1, y_start = ..2)))

# osteotomies_sf <- st_multilinestring(osteotomy_df$grade_1)

hook_sf <- st_multipolygon(pedicle_hook_df$hook)

 ggdraw() +
  draw_image(image = spine_png, x = 0, y = 0, width = 1, valign = 0, clip = "on") + 
   geom_sf(data = hook_sf, color = "red")

Coordinate system already present. Adding new coordinate system, which will replace the existing one.

 ggdraw() +
  draw_image(image = spine_png, x = 0, y = 0, width = 1, valign = 0, clip = "on") + 
   # geom_sf(data = sublaminar_band_sf, color = "red") +
   # geom_sf(data = st_union(x =con_b, y = sub_b)) +
   geom_sf(data = sublaminar_band_sf) +
   # geom_sf(data = sub_b) +
   ylim(0.3, 0.9)

Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale.

 ggdraw() +
  draw_image(image = spine_png, x = 0, y = 0, width = 1, valign = 0, clip = "on") + 
   geom_sf(data = all_implants_sf, color = "red")

Coordinate system already present. Adding new coordinate system, which will replace the existing one.